ArticleNature biotechnology2022
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 518 papers.
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Who cites it
518 citing papers in PubMed.
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- From traditional histopathology to virtual staining: deep learning approaches for assessing tissue lesions in farmed fish.Veterinary research communications · 2026Review
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Deep learning-enhanced single-shot triorganelle STED-FLIM imaging of lipid dynamics in living cells.Science advances · 2026Article
- ResolVI: addressing noise and bias in spatial transcriptomics.Nature methods · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
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- Pan-tumor spatial transcriptomics reveals conserved properties of tumor organization.Cell reports. Medicine · 2026Article
- Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus.Nature methods · 2026Article
- All-optical multimodal mapping of single-cell-type-specific metabolic activities via REDCAT.Nature methods · 2026Article
- Iterative multiplex imaging cytometry for cross-species analyses of in situ tissue leukocytes.Journal of immunological methods · 2026Article
- PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology.Nature methods · 2026Article
- Spatially-resolved single-cell imaging of melanoma brain metastases identifies localized immune patterns predictive of immune checkpoint blockade response.Neuro-oncology · 2026Article
- Artificial Intelligence-Powered High-Content Analysis: Methodologies and Applications in Bioactive Compound Discovery from Natural Sources.Molecules (Basel, Switzerland) · 2026Review
- Spatial analysis reveals cellular microenvironments and mechanisms of inflammation and injury in acute interstitial nephritis.Nature communications · 2026Article
- Therapeutic remodeling of the tuberculosis granuloma with 1-methyl-D-tryptophan enhances CD8Proceedings of the National Academy of Sciences of the United States of America · 2026Article
458 more citing papers are in PubMed but not listed here.
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29 authors.
Funding
Abstract
A principal challenge in the analysis of tissue imaging data is cell segmentation-the task of identifying the precise boundary of every cell in an image. To address this problem we constructed TissueNet, a dataset for training segmentation models that contains more than 1 million manually labeled cells, an order of magnitude more than all previously published segmentation training datasets. We used TissueNet to train Mesmer, a deep-learning-enabled segmentation algorithm. We demonstrated that Mesmer is more accurate than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We then adapted Mesmer to harness cell lineage information in highly multiplexed datasets and used this enhanced version to quantify cell morphology changes during human gestation. All code, data and models are released as a community resource.
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